Chaperonin-Ring's Twist is Critical for Folding Activity of Group II Chaperonin

Abstract

Free energy scale is essential for understanding membrane protein folding and for predicting membrane protein structures. Hydrophobicity scales for membrane proteins have been measured experimentally in lipid bilayer and biological membrane. However, they were based on measurement of model peptides. Recently, a new biological scale of water-to-bilayer transfer free energy of 20 amino acids was obtained by measurement in the context of a native b-barrel transmembrane protein OmpLA [Moon and Fleming, 2011]. Here we report results on computational transfer free energy. It is based on an energy function composed of three terms, single-body burial, inter-strand interaction and sequential nearest neighbor contact interaction. Using a mechanics and statistical model, we have computed the full partition function of OmpLA and the transfer free energy of residues. The computed result of free energy scale of 19 amino acid residues correlates well with experimental data (r2 >0.80). In addition, our results indicate that free energy changes are context dependant. Our computational results also show that the occurrence of Arg is depth dependant and is not be overly costly.